Table 1.

Comparative features of DNA fingerprinting technologies

Technique (year)	Typea	Basisb	Resolutionc	Detectiond	Amounte	Throughputf	Costg
RAPD (1990)	CNA	Arbitrary primer PCR amplification	Native electrophoresis	Ethidium bromide staining	>10ng	L: ~20–50 S: ~20	$1–$2
AP-PCR (1990)	CNA	Arbitrary primer PCR amplification	Denaturing electrophoresis	Autoradiography, silver staining or fluorescence	>10ng	L: ~50–100 S: ~40	$2–$3
CHAPA (2001)	CNA	Arbitrary primer PCR amplification	Microarray slides	Fluorescence	>100ng	L: >1,000 S: 2	~$100–$200
RLGS-M (1993)	MET	Digestion with NotI or AscI	Bidimensional electrophoresis	Autoradiography	>1μg	L: ~1,000 S: 1	~$20
MS-AP-PCR (1997)	MET	Arbitrary primer PCR amplification after digestion with HpaII and RsaI	Denaturing electrophoresis	Autoradiography	>100ng*	L: ~50 S: ~40	$3–$4
MSRF (1997)	MET	Arbitrary primer PCR amplification after digestion with BstUI and MseI	Native electrophoresis	Autoradiography	>100ng*	L: ~50 S: ~40	$3–$4
AIMS (2002)	MET	Adaptor-mediated PCR amplification after digestion with SmaI and XmaI	Denaturing electrophoresis	Autoradiography	>100ng*	L: ~50–100 S: ~20	$3–$5
MS-AFLP (2001)	MET	Adaptor-mediated PCR amplification after digestion with NotI and MseI	Denaturing electrophoresis	Autoradiography or fluorescence	>100ng*	L: ~50–100 S: ~20	$3–$5
Array-MS-AFLP (2004)	MET CNA	Adaptor-mediated PCR amplification after digestion with NotI and MseI	Microarray slides	Fluorescence	>1μg	L: ~10,000h S: 2	~$100–$200
OTHER NON-DNA FINGERPRINTING TECHNIQUESi
Agilent CGH arrays	CNA	Hybridization of labeled genomic DNA fragments	Microarray slides	Fluorescence	>500ng	L: 104–106 S: 1–8	~$200–$500
Illumina Goldengate	CNA MET	Hybridization or single nucleotide extension of labeled DNA fragments	Microarray slides	Fluorescence	200ng-1μg	L: 104–106 S: 1–12	~$200–$500
Affimetrix arrays	CNA	Hybridization of labeled genomic DNA fragments	Microarray slides	Fluorescence	>500ng	L: 104–106 S: 1–96	~$200–$500
CHARM	MET	McrBC-fractionated DNA libraries	Microarray slides	Fluorescence	>3μg	L: 44,000 S: 2	~$200

^aCNA: copy number alterations. MET: DNA methylation alterations.

^bKey feature that underlies the method is listed.

^cMethod for resolving DNA sequences. Except RAPD that may use agarose gel electrophpresis, the rest of the fingerprinting techniques use polyacrylamide or derivatives (i.e., sequagel) gel electrophoresis.

^dMethod of detection of the DNA sequences.

^eValues indicate amount of genomic DNA for the initial digestions. Amounts of sample loaded in the electrophesis for the fingerprinting techniques (*) are less (5–10ng).

^fL: loci per sample; S: number of samples per gel. The values given for the fingerprinting techniques

^gThe cost in US dollars per DNA sample is given as an approximation in a wide range (i.e., depending on whether the analysis is by autoradiography or fluorescence). Costs for fingerprinting techniques include the costs of electrophoresis but not the costs of sample DNA preparation. Costs can be calculated per Mb of genome covered by the techniques, by increasing the number of experiments with different primers. For instance, a map by AP-PCR of random genome sites at a 10Mb resolution for copy number alterations that could provide panoramic views of the degree of disruption of the cancer genome would cost around 6 (primers) X $2–3 = ~$15 per sample, and a map by MS-AFLP of NotI sites at ~10Mb resolution for DNA methylation alterations would cost around 6 (primers) X $3–$5 = ~$25. To reach 1Mb resolution would cost 10 times more, without counting the labor. More than 1Mb resolution would be impractical for DNA fingerprinting technologies.

^hThe current limitation is imposed by the number of NotI sites in the genome, not by the technique itself.

ⁱThe list is not exhaustive, and is only intended to contrast some differences in throughput and cost for comparative purposes. Massive sequencing approaches (i.e., Illumina Solexa Technology, Roche 454 or Applied Biosystems SOLiD) are not included because it is difficult to calculate the cost per sample depending on the extent of the analysis.